Daniel G. MacArthur

The paper identifies discordant genotype calls across sequencing methods in gnomAD, provides a blacklist of problematic variants, and introduces a classifier to detect such variants in other datasets.

The paper identifies PIK3R3 as a candidate regulator of platelet count in Bangladeshi ancestry individuals through GWAS and functional analysis.

The paper cautions against interpreting a yeast study claiming synonymous mutations are as disease-causing as nonsynonymous ones, given existing evidence for their predominant neutrality in humans.

The paper performs single-variant and gene-based association analyses of 4,529 phenotypes using exome data from 426,370 UK Biobank individuals, finding associations linked to variant frequency and deleteriousness.

The paper uses long-read RNA-seq data to identify new transcripts and develop a tool to analyze genetic effects on transcript structure, revealing insights into splicing regulation and variant interpretation.

seqr is a web-based tool for analyzing rare disease genomic data, enabling variant filtering, annotation, and collaboration, with over 10,000 families analyzed and 300 novel disease genes discovered.

The paper presents a pipeline to call mitochondrial DNA variants in gnomAD, reporting population frequencies for 10,850 unique mtDNA variants across 56,434 individuals.

The paper describes the role of the Centers for Mendelian Genomics in advancing gene discovery through data sharing, collaboration, and resource development over the past decade.

The paper uses supervised learning to fine-map cis-eQTLs, identifying 20,913 additional putative causal eQTLs and 310 candidate genes.

This study performs whole genome sequencing of human embryonic stem cells to identify genetic variants and provides resources for cell line selection.

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

The paper quantifies protein levels across 32 human tissues and compares them to transcriptome data, revealing insights into post-transcriptional regulation and disease mechanisms.

This study evaluates genome sequencing as a single diagnostic approach for fetal structural anomalies, showing it detects nearly all variants from standard tests and provides higher diagnostic yield than individual tests.

The paper identifies dispersed duplications and de novo structural mutations using whole-genome sequencing data from 706 families by analyzing IBD relationships and copy number variations.

The paper identifies a healthy individual with complete HAO1 knockout, showing normal oxalate levels but elevated glycolate, supporting the safety of HAO1 inhibition for PH1 therapy.

The paper identifies genetic variants associated with nanophthalmos in an Australian cohort, linking them to clinical features like axial length and hyperopia.

ANEVA quantifies genetic regulatory variation using allelic expression data, improving transcriptome analysis and aiding in rare disease diagnosis.

GTEx v8 maps expression and splicing QTLs in 49 tissues from 838 donors: cis-eQTLs cover 94.7% of protein-coding genes, and cross-tissue QTL sharing mirrors cell-type composition.

ELGH is a population genomics study of British-Bangladeshi and British-Pakistani people in east London, combining health records with genetic data to study disease and genetic influences.

This paper introduces Linked-Reads as a method to comprehensively analyze genome variation, showing it can detect both small and large variants and reconstruct haplotypes more effectively than short-read sequencing.

The paper responds to a critique of their variant filtering method, demonstrating its robustness and highlighting the benefits of using high-resolution variant frequencies for clinical genome interpretation.

This study identifies genetic mutations in 78% of Diamond-Blackfan anemia patients using whole exome sequencing, finds new RP genes, and reports genotype-phenotype associations.

STRetch detects pathogenic short tandem repeat expansions in whole genome sequencing data, revealing novel disease-causing STRs with low false discovery rate.

The paper identifies non-coding mutations as a significant cause of RPGRIP1-mediated inherited retinal degeneration in patients with single coding mutations.

Per-sample assembly with gVCF output, followed by joint genotyping, lets GATK HaplotypeCaller scale linearly with cohort size while calling indels more accurately than SAMtools, UnifiedGenotyper or Platypus.

The paper introduces a new synthetic-diploid benchmark for variant calling accuracy, derived from de novo PacBio assemblies of homozygous human cell lines to reduce bias in error rate estimation.

The paper quantifies mutational intolerance near splice sites, showing specific reference alleles are sensitive to mutations and linked to lower spliced transcript levels and Mendelian mutations.